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phangorn (version 1.2-0)

Phylogenetic analysis in R

Description

Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)

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Version

Install

install.packages('phangorn')

Monthly Downloads

21,468

Version

1.2-0

License

GPL (>= 2)

Maintainer

Klaus Schliep

Last Published

November 22nd, 2010

Functions in phangorn (1.2-0)

midpoint

Tree manipulation
getClans

Clans, slices and clips
as.splits

Splits representation of graphs and trees.
upgma

UPGMA and WPGMA
parsimony

Parsimony tree.
lento

Lento plot
NJ

Neighbor-Joining
allTrees

Compute all trees topologies.
Laurasiatherian

Laurasiatherian data (AWCMEE)
Ancestors

tree utility function
designTree

Compute a design matrix
bootstrap.pml

Bootstrap
pmlCluster

Stochastic Partitioning
dfactorial

Arithmetic Operators
splitsNetwork

Phylogenetic Network
yeast

Yeast alignment (Rokas et al.)
distanceHadamard

Distance Hadamard
phyDat

Conversion among Sequence Formats
treedist

Distances between trees
nni

Tree rearrangements.
modelTest

ModelTest
phangorn-package

Phylogenetic analysis in R
SH.test

Shimodaira-Hasegawa Test
dist.hamming

Pairwise Distances from Sequences
pmlPart

Partition model.
ancestral.pml

Ancestral character reconstruction.
pmlMix

Phylogenetic mixture model
pml

Likelihood of a tree.
read.aa

Read Amino Acid Sequences in a File
simSeq

Simulate sequences.
chloroplast

Chloroplast alignment
hadamard

Hadamard Matrices and Fast Hadamard Multiplication